/**
 * 
 */
package jalview.workers;

import java.util.List;

import jalview.api.AlignCalcManagerI;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;

/**
 * Base class for alignment calculation workers 
 * @author jimp
 *
 */
public abstract class AlignCalcWorker implements AlignCalcWorkerI
{
  /**
   * manager and data source for calculations
   */
  protected AlignViewportI alignViewport;
  protected AlignCalcManagerI calcMan;
  protected AlignmentViewPanel ap;
  protected List<AlignmentAnnotation> ourAnnots=null;
  
  public AlignCalcWorker(AlignViewportI alignViewport,
          AlignmentViewPanel alignPanel)
  {
    this.alignViewport = alignViewport;
    calcMan=alignViewport.getCalcManager();
    ap = alignPanel;    
  }
  protected void abortAndDestroy()
  {
    if (calcMan!=null) {
      calcMan.workerComplete(this);
    }
    alignViewport=null;
    calcMan=null;
    ap=null;
    
  }
  public boolean involves(AlignmentAnnotation i)
  {
    return ourAnnots!=null && ourAnnots.contains(i);
  }

  /**
   * permanently remove from the alignment all annotation rows managed by this worker
   */
  @Override
  public void removeOurAnnotation()
  {
    if (ourAnnots!=null && alignViewport!=null)
    {
      AlignmentI alignment=alignViewport.getAlignment();
      synchronized (ourAnnots) {
        for (AlignmentAnnotation aa:ourAnnots)
        {
          alignment.deleteAnnotation(aa, true);
        }
      }
    }
  }
  // TODO: allow GUI to query workers associated with annotation to add items to annotation label panel popup menu

}